Project info

Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)

Filtering samples:
- C6_2h_3
- PC-12_8h_3
- C6_0.5h_1
- C6_0.5h_2 - C6_0.5h_3

Normalization: Viral read count

Only those reads were counted, where LoRTIA found 3-prime polyA sequences !

1. Counts based on TES only (3` -ends of reads)

Statistics of counts

Difference from mean

Varcoeff

ORF kinetics, according to literature-based kinetic classes

Time-dependent normalized ORF counts (based on TSSs and TES clusters)

Mean and SD with linear connection

Each replicate with loess

Mean and SD with loess function

Combine Kinetic classes

sum up all the (normalized) gene counts for each kinetic class in each sample (replicate) then take the mean and SD of the sums for each hpi and cell line

Literature clusters

Literature Clusters and Selected Genes

Reps with loess and confidence

Means with SD and linear connection

Gene-pair ratios

These pairs were analyzed: ie180/us1, ie180/ep0, us1/ep0, noir1/noir2, noir1/ie180, noir2/ie180

Means with SD and linear connection

Reps with loess and confidence

Sums with linear connection